Examples with InsertSizeMetrics picard.analysis.InsertSizeMetrics used on opensource projects

Example 6 with InsertSizeMetrics

use of picard.analysis.InsertSizeMetrics in project gridss by PapenfussLab.

the class InsertSizeDistribution method create.

public static InsertSizeDistribution create(File insertSizeMetricsFile) {
    InsertSizeDistribution result = null;
    if (insertSizeMetricsFile != null && insertSizeMetricsFile.exists()) {
        FileReader reader = null;
        try {
            reader = new FileReader(insertSizeMetricsFile);
            MetricsFile<InsertSizeMetrics, Integer> file = new MetricsFile<InsertSizeMetrics, Integer>();
            file.read(reader);
            result = InsertSizeDistribution.create(file.getHistogram());
        } catch (FileNotFoundException e) {
            log.error("Missing insert size distribution for ", insertSizeMetricsFile);
        } finally {
            CloserUtil.close(reader);
        }
        if (result == null) {
            log.debug("Unable to extract insert size distribution from ", insertSizeMetricsFile);
        }
    }
    return result;
}

Example 7 with InsertSizeMetrics

use of picard.analysis.InsertSizeMetrics in project gridss by PapenfussLab.

the class IdsvSamFileMetricsTest method wrapper_inner_metrics.

@Test
public void wrapper_inner_metrics() {
    IdsvMetrics im = new IdsvMetrics();
    InsertSizeMetrics ism = new InsertSizeMetrics();
    MapqMetrics mqm = new MapqMetrics();
    List<CigarDetailMetrics> sc = new ArrayList<CigarDetailMetrics>();
    InsertSizeDistribution isd = new InsertSizeDistribution(new int[] { 1 }, new double[] { 1 });
    IdsvSamFileMetrics metrics = new IdsvSamFileMetrics(ism, im, mqm, isd, sc);
    assertEquals(im, metrics.getIdsvMetrics());
    assertEquals(isd, metrics.getInsertSizeDistribution());
    assertEquals(ism, metrics.getInsertSizeMetrics());
    assertEquals(sc, metrics.getCigarDetailMetrics());
    assertEquals(mqm, metrics.getMapqMetrics());
}